Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols Used xiii 1. The Importance of Islands 3 2. Area and Number of Speicies 8 3. Further Explanations of the Area-Diversity Pattern 19 4. The Strategy of Colonization 68 5. Invasibility and the Variable Niche 94 6. Stepping Stones and Biotic Exchange 123 7. Evolutionary Changes Following Colonization 145 8. Prospect 181 Glossary 185 References 193 Index 201

The Theory of Island Biogeography

https://www.cs.princeton.edu/~schapire/papers/ecolmod.pdf

Maximum entropy modeling of species geographic distributions

Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

Computational evolutionary biology, statistical phylogenetics and coalescent-based population genetics are becoming increasingly central to the analysis and understanding of molecular sequence data. We present the Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package version 1.7, which implements a family of Markov chain Monte Carlo (MCMC) algorithms for Bayesian phylogenetic inference, divergence time dating, coalescent analysis, phylogeography and related molecular evolutionary analyses. This package includes an enhanced graphical user interface program called Bayesian Evolutionary Analysis Utility (BEAUti) that enables access to advanced models for molecular sequence and phenotypic trait evolution that were previously available to developers only. The package also provides new tools for visualizing and summarizing multispecies coalescent and phylogeographic analyses. BEAUti and BEAST 1.7 are open source under the GNU lesser general public license and available at http://beast-mcmc.googlecode.com and http://beast.bio.ed.ac.uk

/pdf/bayesian-phylogenetics-with-beauti-and-the-beast-1-7-2xkb29qdvu.pdf

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

Ecological changes in the phenology and distribution of plants and animals are occurring in all well-studied marine, freshwater, and terrestrial groups These observed changes are heavily biased in the directions predicted from global warming and have been linked to local or regional climate change through correlations between climate and biological variation, field and laboratory experiments, and physiological research Range-restricted species, particularly polar and mountaintop species, show severe range contractions and have been the first groups in which entire species have gone extinct due to recent climate change Tropical coral reefs and amphibians have been most negatively affected Predator-prey and plant-insect interactions have been disrupted when interacting species have responded differently to warming Evolutionary adaptations to warmer conditions have occurred in the interiors of species’ ranges, and resource use and dispersal have evolved rapidly at expanding range margins Observed genetic shifts modulate local effects of climate change, but there is little evidence that they will mitigate negative effects at the species level

https://www.fws.gov/southwest/es/documents/R2ES/LitCited/LPC_2012/Parmesan_2006.pdf

Ecological and Evolutionary Responses to Recent Climate Change

Complex speciation, involving rapid divergence and multiple bouts of post-divergence gene flow, can obfuscate phylogenetic relationships and species limits. In North America, cases of complex speciation are common, due at least in part to the cyclical Pleistocene glacial history of the continent. Scrub-jays in the genus Aphelocoma provide a useful case study in complex speciation because their range throughout North America is structured by phylogeographic barriers with multiple cases of secondary contact between divergent lineages. Here, we show that a comprehensive approach to genomic reconstruction of evolutionary history, i.e., synthesizing results from species delimitation, species tree reconstruction, demographic model testing, and tests for gene flow, is capable of clarifying evolutionary history despite complex speciation. We find concordant evidence across all statistical approaches for the distinctiveness of an endemic southern Mexico lineage (A. w. sumichrasti), culminating in support for the species status of this lineage under any commonly applied species concept. We also find novel genomic evidence for the species status of a Texas endemic lineage A. w. texana, for which equivocal species delimitation results were clarified by demographic modeling and spatially explicit models of gene flow. Finally, we find that complex signatures of both ancient and modern gene flow between the non-sister California Scrub-Jay (A. californica) and Woodhouse's Scrub-Jay (A. woodhouseii), result in discordant gene trees throughout the species' genomes despite clear support for their overall isolation and species status. In sum, we find that a multi-faceted approach to genomic analysis can increase our understanding of complex speciation histories, even in well-studied groups. Given the emerging recognition that complex speciation is relatively commonplace, the comprehensive framework that we demonstrate for interrogation of species limits and evolutionary history using genomic data can provide a necessary roadmap for disentangling the impacts of gene flow and incomplete lineage sorting to better understand the systematics of other groups with similarly complex evolutionary histories.

Combining Species Delimitation, Species Trees, and Tests for Gene Flow Clarifies Complex Speciation in Scrub-Jays.

This article is the copyright property of the Entomological Society of America and may not be used for any commercial or other private purpose without specific written permission of the Entomological Society of America

Distribution of members of *Anopheles quadrimaculatus* Say s.l. and implications for their roles in malaria transmission in the United States

We point out complications inherent in biodiversity inventory metrics when applied to large-scale datasets. The number of units of inventory effort (e.g., days of inventory effort) in which a species is detected saturates, such that crucial numbers of detections of rare species approach zero. Any rare errors can then come to dominate species richness estimates, creating upward biases in estimates of species numbers. We document the problem via simulations of sampling from virtual biotas, illustrate its potential using a large empirical dataset (bird records from Cape May, NJ, USA), and outline the circumstances under which these problems may be expected to emerge.

Inventory statistics meet big data: complications for estimating numbers of species.

perspectives ISSN 1948-6596 Phylogeography is not enough: The need for multiple lines of evidence A. Townsend Peterson Biodiversity Research Center, The University of Kansas, Lawrence, Kan- sas 66045 USA e-mail: town@ku.edu; http://specify5.specifysoftware.org/Informatics/ bios/biostownpeterson/ Figure 1. Temperature and precipitation fluctuations over the past 135,000 yr: shown are annual mean temperature profiles (all on the same scale) for the present day, Last Glacial Maximum (21,000 yr ago; CCSM scenario), and Last Interglacial (135,000 yr ago; Otto-Bliesner et al. 2006). The 10 shading classes cover equal intervals between -50° and +31.5°C. Last Glacial Maximum Present day date translated into detailed analyses of key events structuring biogeographic patterns in many phylogeographic analyses. In particular, the Pleistocene was character- ized by a complex series of warm periods (similar to present-day climates) and cold periods (“ice ages”), with impressively short transitions in be- tween (Figure 2; Dansgaard et al. 1993). Although considerable attention has focused on the last of the glacial maxima (~21,000 yr before present), in reality, all of these alternating periods of warm and cold climates probably had some influence on present patterns of diversity and distribution of biodiversity (Svenning and Skov 2004). The pur- pose of this commentary is to reflect on likely ef- fects of such repeated and dramatic global climate fluctuations in shaping patterns of distribution of species, and to emphasize the need for broader Last Interglacial The concepts of equilibrium and stability in bio- geography are perhaps much more fleeting than has generally been appreciated, and disequilib- rium may actually rule the situation in most cases (Manning et al. 2009). That is, although research- ers may discuss current distributional patterns as fixed, those patterns may have been in place only for a relatively short period of time (~10 4 yr), per- haps since the last major global cool period at the end of the Pleistocene (Figure 1). Although Pleis- tocene climatic fluctuations have been considered a major force in biogeography, and some have argued that they may have produced much of cur- rent species diversity (Mengel 1970, Haffer 1997), the validity of the Pleistocene speciation paradigm has been debated hotly recently—see, e.g., Klicka and Zink (1997) versus Weir and Schluter (2004). “The Pleistocene” is often cited as a bio- geographic force, but too often uncritically and without full consideration of the complexity of world climates over the past million years. That is, molecular systematists frequently use molecular “clocks” that date splitting events imprecisely, usually with confidence intervals so broad as to inspire concern (Peterson 2007); these studies often refer to Pleistocene climatic fluctuations, but with no specifics, although the ability to date splitting events may improve with broader use of population-genetic approaches to the challenge (Arbogast et al. 2002). This general appreciation of the role of Pleistocene climatic fluctuations as im- portant biogeographically nonetheless has not to frontiers of biogeography 1.1, 2009 — © 2009 the authors; journal compilation © 2009 The International Biogeography Society

/pdf/perspective-phylogeography-is-not-enough-the-need-for-22sqcobgbg.pdf

perspective: Phylogeography is not enough: The need for multiple lines of evidence

Snow Pigeons live in flocks during the non-breeding season, from mid-October to mid-June (Table 1), and forage on riverbanks and in valley-bottom barley fields, roosting on precipitous cliffs. Cheng et al. (1983) reported that this species occurs at 2,900-3,900m, but I found them up to 4,500m. Grimmett et al. (1998) gives 3,000-5,200 m (occasionally to 5,700 m) as the altitude in summer for this species. A nesting attempt was recorded in Xiong Se valley (29o27 ́N 91o40 ́E), 30 km from Lhasa city. The nest-site was located at 4,020 m on a low cliff, 2.5 m above the ground, next to a stream. On 6 May 2001, I discovered an almost-complete nest, and saw both parents collecting nest material 50 m from the nest-site. The nest was simply constructed from thin roots lined with grass stems, and measured 23.5 cm in diameter, 13.0 cm in depth and 10.5 cm in height. I returned on 29 May and found two chicks, with yellow down and open eyes, being brooded. I measured and weighed them, and repeated this on 4 June (Table 2). On 5 June, the two chicks were found dead below the nest-site having fallen out during a storm the previous night.

A. Townsend Peterson

Papers

Combining Species Delimitation, Species Trees, and Tests for Gene Flow Clarifies Complex Speciation in Scrub-Jays.

Distribution of members of Anopheles quadrimaculatus Say s.l. and implications for their roles in malaria transmission in the United States

Inventory statistics meet big data: complications for estimating numbers of species.

perspective: Phylogeography is not enough: The need for multiple lines of evidence

Delayed plumage maturation in Asian thrushes, genus Turdus